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- PDB-9dtf: Crystal structure of the complex of M. tuberculosis PheRS with co... -

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Basic information

Entry
Database: PDB / ID: 9dtf
TitleCrystal structure of the complex of M. tuberculosis PheRS with cognate precursor tRNA and fragment DDD01008876
Components
  • (Phenylalanine--tRNA ligase ...) x 2
  • tRNA(Phe)
KeywordsLIGASE/RNA / AMINOACYLATION / PHENYLALANYL TRNA SYNTHETASE / STRUCTURAL GENOMICS / LIGASE-TRNA COMPLEX / CENTER FOR STRUCTURAL BIOLOGY OF INFECTIOUS DISEASES / CSBID / LIGASE / LIGASE-RNA complex
Function / homology
Function and homology information


phenylalanine-tRNA ligase complex / phenylalanine-tRNA ligase / phenylalanyl-tRNA aminoacylation / phenylalanine-tRNA ligase activity / peptidoglycan-based cell wall / tRNA binding / magnesium ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Phenylalanine-tRNA ligase, class II, N-terminal / Phenylalanine-tRNA ligase alpha chain 1, bacterial / Aminoacyl tRNA synthetase class II, N-terminal domain / Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type / Phenylalanyl-tRNA synthetase, class IIc, alpha subunit / Phenylalanly tRNA synthetase, tRNA-binding-domain / tRNA synthetase, B5-domain / tRNA synthetase B5 domain / B5 domain profile. / tRNA synthetase B5 domain ...Phenylalanine-tRNA ligase, class II, N-terminal / Phenylalanine-tRNA ligase alpha chain 1, bacterial / Aminoacyl tRNA synthetase class II, N-terminal domain / Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type / Phenylalanyl-tRNA synthetase, class IIc, alpha subunit / Phenylalanly tRNA synthetase, tRNA-binding-domain / tRNA synthetase, B5-domain / tRNA synthetase B5 domain / B5 domain profile. / tRNA synthetase B5 domain / Ferrodoxin-fold anticodon-binding domain / Ferrodoxin-fold anticodon-binding domain superfamily / Ferredoxin-fold anticodon binding domain / B3/4 domain / Ferredoxin-fold anticodon binding (FDX-ACB) domain profile. / Ferredoxin-fold anticodon binding domain / Phenylalanyl tRNA synthetase beta chain, core domain / Phenylalanyl tRNA synthetase beta chain CLM domain / Phenylalanine-tRNA ligase, class IIc, beta subunit / B3/B4 tRNA-binding domain / Phenylalanyl-tRNA synthetase-like, B3/B4 / B3/4 domain / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Putative DNA-binding domain superfamily / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
: / ACETATE ION / TRIETHYLENE GLYCOL / : / RNA / RNA (> 10) / Phenylalanine--tRNA ligase beta subunit / Phenylalanine--tRNA ligase alpha subunit
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsChang, C. / Michalska, K. / Forte, B. / Baragana, B. / Gilbert, I.H. / Wower, J. / Joachimiak, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Eur.J.Med.Chem. / Year: 2025
Title: Different chemical scaffolds bind to L-phe site in Mycobacterium tuberculosis Phe-tRNA synthetase.
Authors: Gade, P. / Chang, C. / Pryde, D.S. / Fletcher, D. / Niven, S. / Magalhaes, L.G. / Robinson, D. / Saini, J. / Ibrahim, P.E.G.F. / Forte, B. / Wower, J. / Bodkin, M.J. / Baragana, B. / ...Authors: Gade, P. / Chang, C. / Pryde, D.S. / Fletcher, D. / Niven, S. / Magalhaes, L.G. / Robinson, D. / Saini, J. / Ibrahim, P.E.G.F. / Forte, B. / Wower, J. / Bodkin, M.J. / Baragana, B. / Gilbert, I.H. / Michalska, K. / Joachimiak, A.
History
DepositionSep 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phenylalanine--tRNA ligase alpha subunit
B: Phenylalanine--tRNA ligase beta subunit
C: tRNA(Phe)
D: Phenylalanine--tRNA ligase alpha subunit
E: Phenylalanine--tRNA ligase beta subunit
F: tRNA(Phe)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)305,83845
Polymers302,3936
Non-polymers3,44539
Water17,366964
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40500 Å2
ΔGint-234 kcal/mol
Surface area110630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.686, 64.065, 187.920
Angle α, β, γ (deg.)90.00, 110.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Phenylalanine--tRNA ligase ... , 2 types, 4 molecules ADBE

#1: Protein Phenylalanine--tRNA ligase alpha subunit / Phenylalanyl-tRNA synthetase alpha subunit / PheRS


Mass: 37486.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: pheS, Rv1649, MTCY06H11.14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFU3, phenylalanine-tRNA ligase
#2: Protein Phenylalanine--tRNA ligase beta subunit / Phenylalanyl-tRNA synthetase beta subunit / PheRS


Mass: 88867.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: pheT, Rv1650, MTCY06H11.15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFU1, phenylalanine-tRNA ligase

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RNA chain , 1 types, 2 molecules CF

#3: RNA chain tRNA(Phe)


Mass: 24842.811 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Mycobacterium tuberculosis H37Rv (bacteria)
References: GenBank: 1251771558

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Non-polymers , 9 types, 1003 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-A1BCA / (5S)-7-benzyl-1,3,7-triazaspiro[4.4]nonane-2,4-dione


Mass: 245.277 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H15N3O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#10: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#11: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 964 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: ammonium acetate HEPES pH 7.5 PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Nov 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 124143 / % possible obs: 99.5 % / Redundancy: 10.1 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.047 / Rrim(I) all: 0.156 / Χ2: 1.161 / Net I/σ(I): 7.2 / Num. measured all: 1259678
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.45-2.499.21.35461400.5790.8570.4581.4340.70199.5
2.49-2.549.31.1661520.6480.8870.391.2280.71799.6
2.54-2.599.30.9862050.7430.9230.3311.0370.71899.3
2.59-2.649.40.80161260.8090.9460.270.8480.7499.4
2.64-2.79.20.70361670.8440.9570.2390.7440.75799.6
2.7-2.769.20.62161270.8650.9630.2110.6580.77399.4
2.76-2.838.40.54461800.8780.9670.1960.580.83498.8
2.83-2.99.40.44361190.9090.9760.150.4690.88999.5
2.9-2.9910.30.36662240.9450.9860.1170.3850.90599.9
2.99-3.0910.40.30962010.9520.9880.0990.3250.98999.8
3.09-3.210.50.25961770.9640.9910.0820.2731.09199.8
3.2-3.3210.60.22962050.9630.9910.0720.2411.23299.9
3.32-3.4810.70.19762030.9750.9940.0620.2071.35899.2
3.48-3.669.90.18162230.9680.9920.0590.1911.51599.4
3.66-3.8910.50.1661840.9770.9940.050.1681.67199.2
3.89-4.1911.60.1562350.9790.9950.0450.1571.744100
4.19-4.6111.40.14162840.9750.9940.0430.1481.79699.8
4.61-5.28110.12962270.9790.9950.040.1361.63599.1
5.28-6.6511.20.12162900.9790.9950.0370.1271.45499.2
6.65-5011.30.09664740.9770.9940.030.1011.07899

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
SCALEPACKdata scaling
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→48.64 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 5527 5.08 %
Rwork0.2035 --
obs0.2058 108823 90.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→48.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17379 3126 222 964 21691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00221697
X-RAY DIFFRACTIONf_angle_d0.40330324
X-RAY DIFFRACTIONf_dihedral_angle_d19.3168405
X-RAY DIFFRACTIONf_chiral_restr0.0373573
X-RAY DIFFRACTIONf_plane_restr0.0043468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.480.3547850.28711859X-RAY DIFFRACTION49
2.48-2.510.35671520.2662135X-RAY DIFFRACTION58
2.51-2.540.33791270.25812350X-RAY DIFFRACTION61
2.54-2.570.30381540.25652565X-RAY DIFFRACTION68
2.57-2.60.29571490.25752707X-RAY DIFFRACTION73
2.6-2.640.32311490.25942950X-RAY DIFFRACTION77
2.64-2.680.3131620.25053087X-RAY DIFFRACTION81
2.68-2.720.30931500.26353241X-RAY DIFFRACTION85
2.72-2.760.30381750.25223319X-RAY DIFFRACTION87
2.76-2.80.33881740.25843330X-RAY DIFFRACTION88
2.8-2.850.31741640.25073499X-RAY DIFFRACTION92
2.85-2.90.29172200.23763665X-RAY DIFFRACTION96
2.9-2.960.30081890.23933683X-RAY DIFFRACTION98
2.96-3.020.2691820.23293771X-RAY DIFFRACTION98
3.02-3.090.25951950.22763781X-RAY DIFFRACTION99
3.09-3.160.29261920.22293795X-RAY DIFFRACTION100
3.16-3.240.27122000.22043813X-RAY DIFFRACTION100
3.24-3.320.2842090.21463782X-RAY DIFFRACTION100
3.32-3.420.25672150.21353780X-RAY DIFFRACTION99
3.42-3.530.25292250.20253768X-RAY DIFFRACTION99
3.53-3.660.2321780.20183788X-RAY DIFFRACTION99
3.66-3.810.23881860.18943840X-RAY DIFFRACTION99
3.81-3.980.22882150.18363831X-RAY DIFFRACTION100
3.98-4.190.22232480.17553765X-RAY DIFFRACTION100
4.19-4.450.21991890.173855X-RAY DIFFRACTION100
4.45-4.790.19072040.16233808X-RAY DIFFRACTION100
4.79-5.280.23122000.1713852X-RAY DIFFRACTION99
5.28-6.040.21191940.18323827X-RAY DIFFRACTION99
6.04-7.60.21862330.19033884X-RAY DIFFRACTION100
7.6-48.640.19872120.17483966X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0046-0.0786-0.05090.0870.03230.1465-0.3105-0.0320.03260.1837-0.03730.2951-0.07220.3206-0.87980.47490.15560.293-0.1371-0.29160.4916-12.37517.55793.7971
20.109-0.1450.18420.1534-0.16550.2682-0.02140.1762-0.1803-0.0640.0257-0.1480.23030.38250.00010.39310.02730.01080.3868-0.04470.273727.121-6.444928.7174
30.2332-0.10970.13450.6704-0.11370.2066-0.1703-0.1164-0.03960.26180.134-0.2342-0.37140.0377-0.03720.2966-0.02120.02520.2027-0.00810.142220.44658.291124.1531
40.0838-0.09380.02350.0462-0.07560.2946-0.23610.21320.061-0.1019-0.0352-0.1598-0.30260.1691-0.58750.3765-0.1435-0.07370.2423-0.08330.038724.17682.453832.436
50.60350.2148-0.22080.6916-0.1560.72950.3354-0.23520.28030.4042-0.12170.1364-0.17030.15140.5754-0.0917-0.0203-0.06560.1716-0.02360.031354.11721.71069.8651
60.6183-0.0067-0.33440.1054-0.01110.2836-0.1962-0.045-0.2785-0.0450.0339-0.13780.2344-0.0046-0.34450.14540.0839-0.01560.25890.09550.157250.5026-0.41292.3438
70.35790.0135-0.1981-0.0081-0.0020.05770.01050.1663-0.07610.01890.0575-0.09080.1936-0.08840.00440.2482-0.0226-0.00180.2125-0.00170.210919.54720.989715.8555
80.5507-0.02970.32810.3535-0.46940.7740.09870.2585-0.0087-0.1901-0.0108-0.02690.17690.23860.09520.36320.0425-0.03660.1454-0.04850.166330.6602-12.316249.2513
90.1806-0.0425-0.03940.68610.09870.26070.00960.0263-0.02360.12320.07420.26750.19-0.01420.59320.2625-0.0353-0.04750.06550.03810.270612.7051-21.31270.933
100.11810.213-0.19120.436-0.40780.3528-0.04690.1024-0.1119-0.7310.1256-0.11030.05410.12120.37570.5055-0.1230.38770.4428-0.09170.401858.30735.144543.7553
110.2666-0.03420.1668-0.0129-0.02190.0689-0.0618-0.05280.538-0.21040.1242-0.5023-0.01430.56740.02510.2851-0.02050.18840.4575-0.1020.532661.32619.15159.3488
120.30910.3865-0.02381.14030.22140.5773-0.3448-0.3546-0.17140.11140.4124-0.61540.3220.3235-0.05010.26250.1648-0.06240.3857-0.01670.212146.35510.27674.6256
130.0221-0.0173-0.01920.0210.02590.02680.0999-0.1383-0.00470.06560.16910.11930.30720.3514-00.50940.10820.15770.7818-0.09560.729269.4431-6.324650.6443
140.00220.0067-0.00080.0167-0.0017-0.0037-0.19910.1496-0.0789-0.16620.08720.0471-0.3603-0.031-01.08290.19830.06510.7787-0.05240.599854.80514.547136.5962
150.7665-0.00030.36560.6813-0.24780.22820.261-0.5443-0.0091-0.1353-0.02760.09380.29560.45030.31930.3613-0.0049-0.03460.6356-0.16820.129163.8203-11.115572.4387
160.2702-0.1648-0.0490.4845-0.03810.7508-0.090.0783-0.09920.1318-0.05230.2272-0.0495-0.357-0.25060.2325-0.0228-0.09810.2632-0.06580.3245-10.25490.875844.5458
170.28460.1777-0.00840.05940.00280.55880.05530.1304-0.2409-0.1076-0.0398-0.03310.3952-0.2132-0.15830.2904-0.0268-0.10910.2282-0.06290.3291-13.3867-7.145140.1732
180.49810.2776-0.02370.63520.15670.11670.4518-0.2801-0.73090.5975-0.14740.13170.86730.10130.55130.382-0.5727-0.26110.51420.32640.5248-46.2573-29.822442.0546
191.25050.34720.42051.0536-0.11180.97380.2426-1.04530.12130.2854-0.01010.32960.0419-0.40272.06060.2215-0.17310.06710.8876-0.09850.2472-48.2503-6.598830.3288
200.24270.0521-0.09720.10640.40610.81580.03940.1014-0.0051-0.082-0.06070.2411-0.1305-0.28220.11920.29020.0218-0.14630.1508-0.00090.4255-5.07839.600759.091
210.3822-0.1344-0.11930.94620.23990.4148-0.070.05430.07190.00530.11780.1174-0.11190.00960.19250.265-0.0067-0.08580.0734-0.02720.130121.367419.222368.7444
220.0503-0.02840.02650.0023-0.01230.0416-0.01520.0420.056-0.46810.00430.0788-0.0812-0.33720.0050.5628-0.03740.05240.5735-0.02491.2683-33.1863-8.201273
230.0811-0.0025-0.13960.02990.07020.2566-0.1299-0.16850.01420.1128-0.19870.3760.0828-0.4342-0.3673-0.12270.02370.44370.5026-0.03521.5758-25.8585-12.42587.1976
240.2128-0.0902-0.19710.14390.17160.2164-0.2581-0.24830.39220.6260.13020.7329-0.1124-0.13840.00030.47830.07070.21390.33640.06750.7199-4.6808-12.522790.8921
250.1453-0.19050.00060.289-0.08030.0915-0.0951-0.05520.0643-0.0444-0.1170.1648-0.1657-0.1736-0.21220.29540.26010.32090.919-0.43241.8409-38.69892.357385.401
260.00660.0029-0.00380.0043-0.00750.0077-0.04020.0309-0.0019-0.0378-0.0038-0.00360.0734-0.023-0.00011.7009-0.0187-0.18961.3972-0.31641.5475-34.6131-7.361364.4138
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 110 )
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 211 )
3X-RAY DIFFRACTION3chain 'A' and (resid 212 through 285 )
4X-RAY DIFFRACTION4chain 'A' and (resid 286 through 341 )
5X-RAY DIFFRACTION5chain 'B' and (resid -2 through 270 )
6X-RAY DIFFRACTION6chain 'B' and (resid 271 through 445 )
7X-RAY DIFFRACTION7chain 'B' and (resid 446 through 516 )
8X-RAY DIFFRACTION8chain 'B' and (resid 517 through 684 )
9X-RAY DIFFRACTION9chain 'B' and (resid 685 through 831 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 10 )
11X-RAY DIFFRACTION11chain 'C' and (resid 11 through 25 )
12X-RAY DIFFRACTION12chain 'C' and (resid 26 through 50 )
13X-RAY DIFFRACTION13chain 'C' and (resid 51 through 65 )
14X-RAY DIFFRACTION14chain 'C' and (resid 66 through 73 )
15X-RAY DIFFRACTION15chain 'D' and (resid 0 through 91 )
16X-RAY DIFFRACTION16chain 'D' and (resid 92 through 242 )
17X-RAY DIFFRACTION17chain 'D' and (resid 243 through 341 )
18X-RAY DIFFRACTION18chain 'E' and (resid -2 through 135 )
19X-RAY DIFFRACTION19chain 'E' and (resid 138 through 486 )
20X-RAY DIFFRACTION20chain 'E' and (resid 487 through 690 )
21X-RAY DIFFRACTION21chain 'E' and (resid 691 through 831 )
22X-RAY DIFFRACTION22chain 'F' and (resid 1 through 10 )
23X-RAY DIFFRACTION23chain 'F' and (resid 11 through 25 )
24X-RAY DIFFRACTION24chain 'F' and (resid 26 through 50 )
25X-RAY DIFFRACTION25chain 'F' and (resid 51 through 65 )
26X-RAY DIFFRACTION26chain 'F' and (resid 66 through 73 )

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